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- EMDB-60998: Cryo-EM structure of an amyloid fibril formed by SOD1 mutant - D101N -

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Basic information

Entry
Database: EMDB / ID: EMD-60998
TitleCryo-EM structure of an amyloid fibril formed by SOD1 mutant - D101N
Map datacryo-em map of an amyloid fibril formed by SOD1 mutant - D101N
Sample
  • Organelle or cellular component: ALS-causing SOD1 mutant D101N
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
KeywordsAmyloid fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / cellular response to cadmium ion / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / glutathione metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / response to amphetamine / thymus development / placenta development / positive regulation of cytokine production / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsZhang MY / Ma YY / Wang LQ / Xia WC / Yuan HY / Zhao K / Chen J / Li D / Zou LY / Wang ZZ ...Zhang MY / Ma YY / Wang LQ / Xia WC / Yuan HY / Zhao K / Chen J / Li D / Zou LY / Wang ZZ / Liu C / Liang Y
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271326 China
National Natural Science Foundation of China (NSFC)32071212 China
National Natural Science Foundation of China (NSFC)31770833 China
National Natural Science Foundation of China (NSFC)32201040 China
CitationJournal: EMBO Rep / Year: 2025
Title: Distinct amyloid fibril structures formed by ALS-causing SOD1 mutants G93A and D101N.
Authors: Mu-Ya Zhang / Yeyang Ma / Li-Qiang Wang / Wencheng Xia / Xiang-Ning Li / Kun Zhao / Jie Chen / Dan Li / Liangyu Zou / Zhengzhi Wang / Cong Liu / Yi Liang /
Abstract: Two hundred eight genetic mutations in SOD1 have been linked to amyotrophic lateral sclerosis (ALS). Of these, the G93A and D101N variants maintain much of their physiological function, closely ...Two hundred eight genetic mutations in SOD1 have been linked to amyotrophic lateral sclerosis (ALS). Of these, the G93A and D101N variants maintain much of their physiological function, closely resembling that of wild-type SOD1, and the SOD1-G93A transgenic mouse is the most extensively used mouse line in the study of ALS. In this study, we report two cryo-EM structures of amyloid fibrils formed by G93A and D101N mutants of SOD1 protein. These mutations give rise to amyloid fibrils with distinct structures compared to native SOD1 fibrils. The fibril core displays a serpentine configuration featuring four β-strands, held together by two hydrophobic cavities and a salt bridge between Arg143 and Asp96 in the G93A fibril, and by a hydrophobic cavity and a salt bridge between Arg143 and Asp132 in the D101N fibril, demonstrating unique structural features for each mutant. Moreover, our results show that G93A fibrils are significantly more toxic than those formed by D101N, which do not show a marked increase in toxicity compared to wild-type SOD1 fibrils. This study sheds light on the structural mechanisms through which SOD1 mutants aggregate and induce cytotoxicity in ALS.
History
DepositionJul 30, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60998.png

Downloads & links

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Map

FileDownload / File: emd_60998.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-em map of an amyloid fibril formed by SOD1 mutant - D101N
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.014533356 - 0.04223633
Average (Standard dev.)0.000067675224 (±0.0008719566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60998_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1 map of D101N fibril

Fileemd_60998_half_map_1.map
Annotationhalf1 map of D101N fibril
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map of D101N fibril

Fileemd_60998_half_map_2.map
Annotationhalf2 map of D101N fibril
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ALS-causing SOD1 mutant D101N

EntireName: ALS-causing SOD1 mutant D101N
Components
  • Organelle or cellular component: ALS-causing SOD1 mutant D101N
    • Protein or peptide: Superoxide dismutase [Cu-Zn]

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Supramolecule #1: ALS-causing SOD1 mutant D101N

SupramoleculeName: ALS-causing SOD1 mutant D101N / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.826576 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ATKAVCVLKG DGPVQGIINF EQKESNGPVK VWGSIKGLTE GLHGFHVHEF GDNTAGCTSA GPHFNPLSRK HGGPKDEERH VGDLGNVTA DKDGVADVSI ENSVISLSGD HCIIGRTLVV HEKADDLGKG GNEESTKTGN AGSRLACGVI GIAQ

UniProtKB: Superoxide dismutase [Cu-Zn]

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 0.48 mg/ml / Component - Name: tris
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.816 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.634 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 104331
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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